The conventional molecular beacons contain a fluorescent organic group and a quenching organic group that are covalently bonded to each of the ends of a single-stranded oligonucleotide having a hair-pin loop structure. When an oligonucleotide having a subject sequence that can form a double strand with the loop region is absent, the fluorescent organic group and the quenching organic group will be located in the vicinity to each other due to a stem structure formed by the sequence of the both ends of the beacons so as to cause Fluorescence Resonance Transfer (FRET). As a result, the emission by the fluorescent organic group will be quenched by the quenching organic group. On the other hand, when the oligonucleotide having the subject sequence co-exist with the molecular beacons, such sequence will form a double strand with the loop region of the molecular beacons so that the fluorescent organic group and the quenching organic group will be located in such a distance that FRET cannot occur. As a result, the emission by the fluorescent organic group will be revived. The beacons may be also used in the detection of SNP wherein a subject oligonucleotide having a complementary sequence except a single base cannot revive the emission by the fluorescent organic group.
The conventional DNA probe molecule based on excimer emission (complex between ground-state and excited state molecules of the same kind of a fluorescent organic molecule, which has emission with a longer wavelength than that of the monomer emission) uses two kinds of proves wherein the proves are covalently bonded to a fluorescent organic group capable of forming the excimer, and form a three-dimensional complex with an oligonucleotide having the subject complementary sequence.    Non-Patent Document 1: Tyagi, S.; Kramer, F. R. Nat. Biotechnol. 1996, 14, 303-308    Non-Patent Document 2: Tyagi, S.; Marras, S. A. E.; Kramer, F. R. Nat. Biotechnol. 2000, 18, 1191-1196    Non-Patent Document 3: Tan, W.; Fang, X.; Li, J.; Liu, X. Chem. Eur. J. 2000, 6, 1107-1111    Non-Patent Document 4: Zhang, P.; Beck, T.; Tan, W.; Angew. Chem., Int. Ed. 2001, 40, 402-405